Automatic detection of quality spectra
View Patent ↗The present application provides systems and/or methods for accessing a portion of a mass-fragment spectrum, constructing a vector that is responsive to an intensity-balance of the spectrum, and selecting the spectrum responsive to the vector.
1. A computer controlled method comprising:
accessing a portion of a mass-fragment spectrum;
evaluating the portion of the mass-fragment spectrum responsive to an intensity balance of the portion of the mass-fragment spectrum; and
processing the mass-fragment spectrum responsive to the step of evaluating.
2. The method of claim 1 , wherein the step of processing further comprises rating the mass-fragment spectrum.
3. The method of claim 1 , wherein the step of processing further comprises selecting the mass-fragment spectrum.
4. The method of claim 1 , wherein the step of evaluating further comprises:
constructing a vector responsive to the intensity balance of the mass-fragment spectrum; and
locating the vector in a multidimensional space comprising a plurality of regions separated by at least one surface, the at least one surface determined by training data.
5. The method of claim 4 , wherein the at least one surface is a quadratic surface.
6. The method of claim 1 , wherein the step of evaluating further comprises:
constructing a vector responsive to the intensity balance of the mass-fragment spectrum;
determining one or more parameters of an evaluation function, the one or more parameters responsive to training data; and
applying the parameterized evaluation function to the vector.
7. The method of claim 6 , wherein the step of determining further comprises application of a support vector machine to the vector and the multidimensional space.
8. The method of claim 1 , further comprising constructing a vector responsive to the intensity balance of the mass-fragment spectrum, and wherein the construction of the vector further includes making the vector responsive to a peak pair difference of the mass-fragment spectrum.
9. The method of claim 1 , further comprising constructing a vector responsive to the intensity balance of the mass-fragment spectrum, and wherein the vector is responsive to a normalized intensity of pairs of peaks with m/z values differing by approximately 18 Da.
10. The method of claim 9 , wherein the normalizing step includes using a rank-based intensity normalization scheme.
11. The method of claim 1 , wherein the mass-fragment spectrum is of a sample containing a polymer.
12. The method of claim 11 , wherein the polymer is selected from one or more of the group consisting of a peptide, a polysaccharide, a lipid and a polynucleotide.
13. The method of claim 1 , wherein the mass-fragment spectrum includes at least one peak which represents a multiply charged ion.
14. A program product comprising:
a computer-usable data carrier storing instructions that, when executed by a computer, cause said computer to perform a method comprising:
accessing a portion of a mass-fragment spectrum;
evaluating the portion of the mass-fragment spectrum responsive to an intensity balance of the portion of the mass-fragment spectrum; and
processing the mass-fragment spectrum responsive to the step of evaluating.
15. The program product of claim 14 wherein the step of processing further comprises rating or selecting the mass-fragment spectrum.
16. The method of claim 14 , wherein the step of evaluating further comprises:
constructing a vector responsive to the intensity balance of the mass-fragment spectrum; and
locating the vector in a multidimensional space comprising a plurality of regions separated by at least one surface, the at least one surface determined by training data.
17. The method of claim 14 , wherein the step of evaluating further comprises:
constructing a vector responsive to the intensity balance of the mass-fragment spectrum;
determining one or more parameters of an evaluation function, the one or more parameters responsive to training data; and
applying the parameterized evaluation function to the vector.
18. An apparatus comprising:
a mass spectrometer that generates a mass-fragment spectrum; and
a computer that employs a filter that accesses at least a portion of the mass-fragment spectrum, constructs a vector that is responsive to an intensity-balance of the spectrum, and selects the spectrum responsive to the vector.
19. The apparatus of claim 18 , further comprising a sequencer that determines at least one possible sequence of a plurality of molecular subunits that corresponds to the information in the mass-fragment spectrum.
20. A computer controlled method comprising:
accessing a portion of a mass-fragment spectrum;
evaluating the portion of the mass-fragment spectrum responsive to a peak pair difference; and
processing the mass-fragment spectrum responsive to the step of evaluating.
21. The method of claim 20 , wherein the step of processing further comprises rating the mass-fragment spectrum.
22. The method of claim 20 , wherein the step of processing further comprises selecting the mass-fragment spectrum.
23. The method of claim 20 , wherein the step of evaluating further comprises
constructing a vector responsive to the peak pair difference; and
locating the vector in a multidimensional space comprising a plurality of regions separated by at least one surface, the at least one surface determined by training data.
24. The method of claim 23 , wherein the at least one surface is a quadratic surface.
25. The method of claim 20 , wherein the step of evaluating further comprises:
constructing a vector responsive to the peak pair difference;
determining one or more parameters of an evaluation function, the one or more parameters responsive to training data; and
applying the parameterized evaluation function to the vector.
26. The method of claim 25 , wherein the evaluation function is a linear function of the vector.
27. The method of claim 25 , wherein the evaluation function is a polynomial function of the vector.
28. The method of claim 20 , wherein the step of determining further comprises
constructing a vector responsive to the peak pair difference; and
application of a support vector machine to the vector.
29. The method of claim 20 , wherein the peak pair difference is a difference between a peak isotope pair.
30. The method of claim 20 , wherein the step of evaluating is also responsive to an intensity balance of the mass-fragment spectrum.
31. The method of claim 20 , wherein the peak pair difference is of a pair of peaks with m/z values differing by approximately 18 Da.
32. The method of claim 20 , wherein the step of evaluating is also responsive to a normalized intensity of pairs of peaks,
33. The method of claim 32 , wherein normalizing intensity peaks includes using a rank-based intensity normalization scheme.
34. The method of claim 20 , wherein the mass-fragment spectrum is of a sample containing a polymer.
35. The method of claim 34 , wherein the polymer is selected from one or more of the group consisting of a peptide, a polysaccha ride 1 a lipid and a polynucleotide.
36. The method of claim 20 , wherein the mass-fragment spectrum includes at least one peak which represents a multiply charged ion.
37. A program product comprising:
a computer-usable data carrier storing instructions that, when executed by a computer, cause said computer to perform a method comprising:
accessing a portion of a mass-fragment spectrum;
evaluating the portion of the mass-fragment spectrum responsive to a peak pair difference; and
processing the mass-fragment spectrum responsive to the step of evaluating.
38. The program product of claim 37 wherein the step of processing further comprises rating or selecting the mass-fragment spectrum.
39. The program product of claim 37 , wherein the step of evaluating further comprises:
constructing a vector responsive to the peak pair difference; and
locating the vector in a multidimensional space comprising a plurality of regions separated by at least one surface, the at least one surface determined by training data.
40. An apparatus comprising:
a mass spectrometer that generates a mass-fragment spectrum; and
a filter that accesses at least a portion of the mass-fragment spectrum, constructs a vector that is responsive to a peak pair difference and selects the spectrum responsive to the vector.
41. The apparatus of claim 40 , further comprising a sequencer that determines at least one possible sequence of a plurality of monomers that corresponds to the information in the mass-fragment spectrum.